Package ubic.gemma.core.analysis.service

Class ExpressionDataFileServiceImpl

java.lang.Object

ubic.gemma.core.analysis.service.AbstractFileService<ExpressionExperiment>

ubic.gemma.core.analysis.service.ExpressionDataFileServiceImpl

All Implemented Interfaces:

ExpressionDataFileService, FileService<ExpressionExperiment>, JsonFileService<ExpressionExperiment>, TsvFileService<ExpressionExperiment>

@Component
@ParametersAreNonnullByDefault
public class ExpressionDataFileServiceImpl
extends AbstractFileService<ExpressionExperiment>
implements ExpressionDataFileService

Supports the creation and location of 'flat file' versions of data in the system, for download by users. Files are cached on the filesystem and reused if possible, rather than recreating them every time.

Author:

paul

Field Summary

Fields inherited from interface ubic.gemma.core.analysis.service.ExpressionDataFileService

DISCLAIMER

Constructor Summary

Constructors

Constructor	Description
ExpressionDataFileServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	analysisResultSetsToString(Collection<ExpressionAnalysisResultSet> results, Map<Long,String[]> geneAnnotations, StringBuilder buf)
List<DifferentialExpressionAnalysisResult>	analysisResultSetToString(ExpressionAnalysisResultSet ears, Map<Long,String[]> geneAnnotations, StringBuilder buf, Map<Long,StringBuilder> probe2String, List<DifferentialExpressionAnalysisResult> sortedFirstColumnOfResults)
void	deleteAllFiles(ExpressionExperiment ee)	Delete any existing coexpression, data, or differential expression data files.
void	deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)
File	getDiffExpressionAnalysisArchiveFile(Long analysisId, boolean forceCreate)	Locate or create the differential expression data file(s) for a given experiment.
File	getMetadataFile(ExpressionExperiment ee, ExpressionExperimentMetaFileType type)	Locate a metadata file.
void	writeDiffExArchiveFile(BioAssaySet experimentAnalyzed, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Writes to the configured gemma.appdata.home The file created is a zip archive containing at least two files.
Optional<File>	writeOrLocateCoexpressionDataFile(ExpressionExperiment ee, boolean forceWrite)	Write or located the coexpression data file for a given experiment
File	writeOrLocateDesignFile(ExpressionExperiment ee, boolean forceWrite)	Locate or create an experimental design file for a given experiment.
Collection<File>	writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee, boolean forceWrite)	Locate or create the differential expression data file(s) for a given experiment.
Optional<File>	writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)
File	writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
Optional<File>	writeOrLocateProcessedDataFile(ExpressionExperiment ee, boolean forceWrite, boolean filtered)	Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
File	writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)	Locate or create a new data file for the given quantitation type.
void	writeProcessedExpressionData(ExpressionExperiment ee, Writer writer)	Write processed expression data to a given writer for a given quantitation type.
Optional<File>	writeProcessedExpressionDataFile(ExpressionExperiment ee, boolean filtered, String fileName, boolean compress)	Create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).
void	writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)	Write raw expression data to a given writer for a given quantitation type.
void	writeTsv(ExpressionExperiment entity, Writer writer)	Write the given entity to tabular format.

Methods inherited from class ubic.gemma.core.analysis.service.AbstractFileService

escapeTsv, format, getSubDelimiter, getTsvFormatBuilder, write, write, writeJson

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.core.analysis.service.FileService

write, write

Constructor Detail

ExpressionDataFileServiceImpl

public ExpressionDataFileServiceImpl()

Method Detail

analysisResultSetsToString

public void analysisResultSetsToString(Collection<ExpressionAnalysisResultSet> results,
                                       Map<Long,String[]> geneAnnotations,
                                       StringBuilder buf)

Specified by:

analysisResultSetsToString in interface ExpressionDataFileService

analysisResultSetToString

public List<DifferentialExpressionAnalysisResult> analysisResultSetToString(ExpressionAnalysisResultSet ears,
                                                                            Map<Long,String[]> geneAnnotations,
                                                                            StringBuilder buf,
                                                                            Map<Long,StringBuilder> probe2String,
                                                                            @Nullable
                                                                            List<DifferentialExpressionAnalysisResult> sortedFirstColumnOfResults)

Specified by:

analysisResultSetToString in interface ExpressionDataFileService

deleteAllFiles

public void deleteAllFiles(ExpressionExperiment ee)

Description copied from interface: ExpressionDataFileService

Delete any existing coexpression, data, or differential expression data files.

Specified by:

deleteAllFiles in interface ExpressionDataFileService

Parameters:

ee - the experiment

deleteDiffExArchiveFile

public void deleteDiffExArchiveFile(DifferentialExpressionAnalysis analysis)

Specified by:

deleteDiffExArchiveFile in interface ExpressionDataFileService

getDiffExpressionAnalysisArchiveFile

public File getDiffExpressionAnalysisArchiveFile(Long analysisId,
                                                 boolean forceCreate)

Description copied from interface: ExpressionDataFileService

Locate or create the differential expression data file(s) for a given experiment. We generate an archive that contains following files: - differential expression analysis file (q-values per factor) - file for each result set with contrasts info (such as fold change for each factor value)

Specified by:

getDiffExpressionAnalysisArchiveFile in interface ExpressionDataFileService

Parameters:

analysisId - analysis ID

forceCreate - whether to force creation

Returns:

file

getMetadataFile

public File getMetadataFile(ExpressionExperiment ee,
                            ExpressionExperimentMetaFileType type)

Description copied from interface: ExpressionDataFileService

Locate a metadata file.

Specified by:

getMetadataFile in interface ExpressionDataFileService

writeProcessedExpressionDataFile

public Optional<File> writeProcessedExpressionDataFile(ExpressionExperiment ee,
                                                       boolean filtered,
                                                       String fileName,
                                                       boolean compress)
                                                throws IOException,
                                                       FilteringException

Description copied from interface: ExpressionDataFileService

Create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only).

Specified by:

writeProcessedExpressionDataFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

filtered - fitlered?

fileName - file name

compress - compress?

Returns:

file, or empty if the experiment has no processed expression data

Throws:

IOException - when there are IO problems

FilteringException

writeDiffExArchiveFile

public void writeDiffExArchiveFile(BioAssaySet experimentAnalyzed,
                                   DifferentialExpressionAnalysis analysis,
                                   @Nullable
                                   DifferentialExpressionAnalysisConfig config)
                            throws IOException

Description copied from interface: ExpressionDataFileService

Writes to the configured gemma.appdata.home The file created is a zip archive containing at least two files. The first is the summary model fit statistics, ANOVA-style. The others are the contrast details for each factor. They should be R-friendly (e.g., readable with read.delim("analysis.results.txt", header=T, comment.char="#", row.names=1)

Specified by:

writeDiffExArchiveFile in interface ExpressionDataFileService

Parameters:

experimentAnalyzed - the experiment

analysis - analysis

config - config

Throws:

IOException - when there was a problem during write

writeRawExpressionData

@Transactional(readOnly=true)
public void writeRawExpressionData(ExpressionExperiment ee,
                                   QuantitationType qt,
                                   Writer writer)
                            throws IOException

Description copied from interface: ExpressionDataFileService

Write raw expression data to a given writer for a given quantitation type.

Note: For compression, wrap a GZIPOutputStream with a OutputStreamWriter. To write to a string, consider using StringWriter.

Specified by:

writeRawExpressionData in interface ExpressionDataFileService

Parameters:

ee - the expression experiment

qt - a quantitation type to use

writer - the destination for the raw expression data

Throws:

IOException - if operations with the writer fails

writeProcessedExpressionData

@Transactional(readOnly=true)
public void writeProcessedExpressionData(ExpressionExperiment ee,
                                         Writer writer)
                                  throws IOException

Description copied from interface: ExpressionDataFileService

Write processed expression data to a given writer for a given quantitation type.

Note: For compression, wrap a GZIPOutputStream with a OutputStreamWriter. To write to a string, consider using StringWriter.

Specified by:

writeProcessedExpressionData in interface ExpressionDataFileService

Parameters:

ee - the expression experiment

writer - the destination for the raw expression data

Throws:

IOException - if operations with the writer fails

writeOrLocateCoexpressionDataFile

public Optional<File> writeOrLocateCoexpressionDataFile(ExpressionExperiment ee,
                                                        boolean forceWrite)

Description copied from interface: ExpressionDataFileService

Write or located the coexpression data file for a given experiment

Specified by:

writeOrLocateCoexpressionDataFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - whether to force write

Returns:

file

writeOrLocateProcessedDataFile

public Optional<File> writeOrLocateProcessedDataFile(ExpressionExperiment ee,
                                                     boolean forceWrite,
                                                     boolean filtered)
                                              throws FilteringException

Description copied from interface: ExpressionDataFileService

Locate or create a data file containing the 'preferred and masked' expression data matrix, with filtering for low expression applied (currently supports default settings only). It will be gzip-compressed. The file will be regenerated even if one already exists if the forceWrite parameter is true, or if there was a recent change (more recent than the last modified date of the existing file) to any of the experiments platforms.

Specified by:

writeOrLocateProcessedDataFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - force re-write even if file already exists and is up to date.

filtered - filtered

Returns:

file, or empty if the experiment has no processed vectors

Throws:

FilteringException

writeOrLocateRawExpressionDataFile

public File writeOrLocateRawExpressionDataFile(ExpressionExperiment ee,
                                               QuantitationType type,
                                               boolean forceWrite)

Description copied from interface: ExpressionDataFileService

Locate or create a new data file for the given quantitation type. The output will include gene information if it can be located from its own file.

Specified by:

writeOrLocateRawExpressionDataFile in interface ExpressionDataFileService

type - the quantitation type

forceWrite - To not return the existing file, but create it anew.

Returns:

file

writeOrLocateDesignFile

public File writeOrLocateDesignFile(ExpressionExperiment ee,
                                    boolean forceWrite)

Description copied from interface: ExpressionDataFileService

Locate or create an experimental design file for a given experiment. The file will be regenerated even if one already exists if the forceWrite parameter is true, or if there was a recent change (more recent than the last modified date of the existing file) to any of the experiments platforms.

Specified by:

writeOrLocateDesignFile in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - force re-write even if file already exists and is up to date

Returns:

file

writeOrLocateDiffExpressionDataFiles

public Collection<File> writeOrLocateDiffExpressionDataFiles(ExpressionExperiment ee,
                                                             boolean forceWrite)

Description copied from interface: ExpressionDataFileService

Locate or create the differential expression data file(s) for a given experiment.

Specified by:

writeOrLocateDiffExpressionDataFiles in interface ExpressionDataFileService

Parameters:

ee - the experiment

forceWrite - whether to force write

Returns:

collection of files, one per analysis.

writeOrLocateJSONProcessedExpressionDataFile

public Optional<File> writeOrLocateJSONProcessedExpressionDataFile(ExpressionExperiment ee,
                                                                   boolean forceWrite,
                                                                   boolean filtered)
                                                            throws FilteringException

Specified by:

writeOrLocateJSONProcessedExpressionDataFile in interface ExpressionDataFileService

Throws:

FilteringException

See Also:

ExpressionDataFileService.writeOrLocateProcessedDataFile(ExpressionExperiment, boolean, boolean)

writeOrLocateJSONRawExpressionDataFile

public File writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee,
                                                   QuantitationType type,
                                                   boolean forceWrite)

Specified by:

writeOrLocateJSONRawExpressionDataFile in interface ExpressionDataFileService

See Also:

ExpressionDataFileService.writeOrLocateRawExpressionDataFile(ExpressionExperiment, QuantitationType, boolean)

writeTsv

@Transactional(readOnly=true)
public void writeTsv(ExpressionExperiment entity,
                     Writer writer)
              throws IOException

Description copied from interface: TsvFileService

Write the given entity to tabular format.

Specified by:

writeTsv in interface TsvFileService<ExpressionExperiment>

Throws:

IOException